ArticleGenome biology2018
SeqOthello: querying RNA-seq experiments at scale.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed.
- Fast and sensitive detection of targeted gene fusions using frequency minimizers and fuzzy pattern matching with Fuzzion2.Cell reports methods · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Usage of the National Cancer Institute Cancer Research Data Commons by Researchers: A Scoping Review of the Literature.JCO clinical cancer informatics · 2024Article
- Indexing and searching petabase-scale nucleotide resources.Nature methods · 2024Article
- Scalable sequence database search using partitioned aggregated Bloom comb trees.Bioinformatics (Oxford, England) · 2023Article
- Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.Genome biology · 2023Article
- Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments.Bioinformatics (Oxford, England) · 2022Article
- SPRISS: approximating frequent k-mers by sampling reads, and applications.Bioinformatics (Oxford, England) · 2022Article
- An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.Bioinformatics (Oxford, England) · 2022Article
- Space-efficient representation of genomic k-mer count tables.Algorithms for molecular biology : AMB · 2022Article
- Data Structures to Represent a Set ofACM computing surveys · 2022Article
- Kmerator Suite: design of specificNAR genomics and bioinformatics · 2021Article
- Simplitigs as an efficient and scalable representation of de Bruijn graphs.Genome biology · 2021Article
- MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata.BMC bioinformatics · 2021Article
- Telomere Roles in Fungal Genome Evolution and Adaptation.Frontiers in genetics · 2021Article
- Data structures based onGenome research · 2021Review
- Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.Genome biology · 2020Article
- REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets.Bioinformatics (Oxford, England) · 2020Article
- An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Improved representation of sequence bloom trees.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.